Proteins that chaperone rna regulation

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Proteins that chaperone RNA regulation
Sarah A. Woodson
1,*
, Subrata Panja
1
, and Andrew Santiago-Frangos
2
1
T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., 
Baltimore, MD 21218 USA
2
Program in Cell, Molecular and Developmental Biology and Biophysics, Johns Hopkins 
University, 3400 N. Charles St., Baltimore, MD 21218 USA
Abstract
RNA-binding proteins chaperone the biological functions of non-coding RNA by reducing RNA 
misfolding, improving matchmaking between regulatory RNA and targets, and exerting quality 
control over RNP biogenesis. Recent studies of 
E. coli CspA, HIV NCp and E. coli Hfq, are 
beginning to show how RNA-binding proteins remodel RNA structures. These different protein 
families use common strategies for disrupting or annealing RNA double helices, which can be 
used to understand the mechanisms by which proteins chaperone RNA-dependent regulation in 
bacteria.
INTRODUCTION
Non-coding RNA sequences fold into useful structures that regulate gene expression as 
ribozymes, metabolite binding sensors, or antisense RNAs (1–5). These regulatory RNAs are 
chaperoned by diverse families of RNA binding proteins, and the loss of RNA chaperone 
proteins can lead to impaired growth, reduced tolerance to stress, and reduced virulence (6–
11). RNA chaperones also facilitate conformational rearrangements during ribosome 
biogenesis (12) and eukaryotic pre-mRNA splicing (13).
These housekeeping and regulatory functions of RNA chaperones are particularly important 
at cold temperatures that hyperstabilize RNA structures. For example, the up-regulation of 
cold shock domain RNA binding proteins during low temperature growth destabilizes RNA 
structures that would otherwise impair transcription elongation and translation initiation at 
low temperatures (14). Moreover, over-expression of cold shock proteins and other RNA 
chaperones buffered deleterious mutations in 
E. coli (15), suggesting that such proteins 
broadly mitigate the effects of RNA misfolding.
RNA chaperones act by transiently binding and releasing RNA substrates, disrupting the 
RNA secondary and tertiary structure (unwinding and unfolding) or accelerating base 
pairing with a second RNA strand (annealing) (16, 17). RNA helices can be actively 
unwound by DEAD-box proteins, which couple unfolding of the RNA structure to ATP 
hydrolysis (18, 19). Bacteria typically encode a handful (0–12) of DEAD-box proteins that 
*
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